Prediction Of Mutation Impact
3
6
Entering edit mode
10.1 years ago
kylejudita ▴ 90

Hi,

am trying to "predict the effect of mutation impact on protein function", am trying to get features to achieve the prediction. I wonder what features I can get using BLAST, BLAST-PSI. I have data for protein sequence, mutation, position of mutation.

mutation • 4.5k views
ADD COMMENT
1
Entering edit mode

This appears to be an almost identical question to your original post: http://www.biostars.org/post/show/48786/blastpgp_mutant_residue and your follow-up question which was deleted as a duplicate: http://www.biostars.org/post/show/48840/looking-for-features-to-predict-mutation-impacts/. Please stop posting the same question.

ADD REPLY
0
Entering edit mode

As Neil said. Just in case you don't know, you can edit your question or post comments to answers if they are not satisfactory to you, but chain posting doesn't help your cause at all.

ADD REPLY
4
Entering edit mode
10.1 years ago
Rm 8.2k

To "predict the effect of mutation impact on protein function": look for servers like polyphen, SIFT, PolyDoms etc...

Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations

ADD COMMENT
2
Entering edit mode

Condel Is a method that gives combined score of polyphen, SIFT etc.

http://bg.upf.edu/condel/home

ADD REPLY
0
Entering edit mode

Thanks, but I still need to find the features, . What features I need to include if , for example, I want to predict the effect of mutation on protein function . I guess it is a matter of experimentation, but there must be a number of features must exist. I currently have WPM, wildtype residue, position, Mutation residue, and protein sequence. I see many papers use Blast, what features I can get when calling Blast? Thanks

ADD REPLY
0
Entering edit mode

Maybe the same features as described in the publications listed here?

ADD REPLY
0
Entering edit mode

@Michael: Link is missing

ADD REPLY
0
Entering edit mode

Sorry for the misunderstanding, with here I meant in the respective publications of the tools found in the answer by Rm given above. In principle, choosing the same features as SIFT of Polyphen.

ADD REPLY
0
Entering edit mode

Got it. :) :) :)

ADD REPLY
4
Entering edit mode
10.1 years ago
Dataminer ★ 2.7k

Hi!

As Rm suggested, you can use SIFT, PolyPhen, I-mutant, CUPSAT, CONDEl etc.

It all depends what you want as an end result and the approach you want to adapt.

ADD COMMENT
0
Entering edit mode
19 months ago
Shicheng Guo ★ 9.1k

AlphaFold V2 increase protein 3D structure prediction accuracy to next level (~90%). AlphaFold received a very high score which is around 90, even for some worst situation, distance score test come up to 80+. You can try to take genetic variants into the model and check what will happen to the new 3D structure. https://deepmind.com/research/open-source/alphafold_casp13

ADD COMMENT

Login before adding your answer.

Traffic: 1498 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6